The Heirs of Atlantis
by shannyfish
Summary: The people of Atlantis become concerned and curious when things start to happen to Atlantis and strangers appear...
1. Chapter 1 The Little Princess

**Author:** atlantis child/innocent choir girl

**Title:** The Heirs to Atlantis

**Chapter Title:** Chapter 1 "The Little Princess"

**Summary:** Major Sheppard and Doctor Weir are quite confused at new arrivals that appear on Atlantis. They know too much for strangers.

**Genres:** Alternate Universe, Angst, Drama, Future Fic

**Rating:** PG

**Warnings:** none

**Author's note: **okay, I know I spelled Anthosian wrong in this chapter I apoligize ahead of time for it!

Atlantis' glow amazed her, it was so beautiful. It was also comforting in a way. She wasn't sure how. But she knew it was. She could feel it. A smile spread across her face. It was like a wonderland…all the lights that seemed to be painted into the room.

"IDENTIFY YOURSELF!"

Her green eyes widened as she saw the weapons pointed towards her. She just froze, standing there. Not knowing what exactly to do, tears rolled down her cheeks. Why were there weapons pointed at her! She didn't do anything wrong! She hadn't even done so much as to touch anything…just admire.

"IDENTIFY YOURSELF!"

"Sergeant! I think that's enough!" Doctor Weir yelled at Atlantis' chief of security. She hurried down the stairs.

"She appeared out of nowhere, Ma'am! Won't identify herself!" Sergeant Bates reported.

Elizabeth pushed his weapon down, "Probably because you've scared the poor girl," she told him. She turned to the small girl and smiled at her, "Hello there." When the girl didn't speak, Elizabeth walked towards her and kneeled down so she was at her level. "My name is Elizabeth, what's yours?"

Again, Elizabeth waited, but the girl didn't answer. She studied the girl in the silence; she figured she couldn't be more than seven years old. She was curious as to the child's attire; she was dressed in all white. A tunic-like top and pant bottoms, her shoes even matched. Her hair was short, above her shoulders and a brownish red color. Her eyes were a vibrant green, but Elizabeth could see fear and worry in them.

"I bet Sergeant Bates scared you, didn't he? He was just…surprised. Can you tell me how you got here?"

The girl shook her head, her hair swaying a bit. A worried look still etched across her face.

"Can you at least tell me your name?" Elizabeth asked hoping to at least get one piece of information. At least with a name she could try to further her relationship with the child and possibly get more information.

The girl studied the woman for a minute before finally replying in a tiny voice. She was quiet and acted in quite a shy manner, "Zaira."

"Zaira? That's a beautiful name," she said smiling at her. Elizabeth straightened and held out her hand, "How about we go for a little walk."

Zaira nodded and took the woman's hand. This…Elizabeth seemed like a nice enough person. She could trust her, couldn't she? She sensed she could. "Zaira means princess."

"Does it?" she asked smiling down at the girl leading her away from the Stargate and wanting to get her to see Doctor Beckett. Elizabeth was happy that at least she knew the girl's name and that she could talk, but there were far more questions that needed answering.

"I don't like this room," Zaira said frowning as they reached right outside of the medical bay. She backed up a bit still frowning at the doors of the place. "Can we go somewhere else?"

"No, my friend, remember? His name is Carson. I wanted him to meet you," she told the child and wrapped her arm around her before using a tad more force to get the girl into the medical bay. "There. That wasn't so bad, was it?"

Zaira shuddered, "I don't like this place."

"A lot of people don't, lass," Carson said smiling at the girl, his Scottish accent thick as he spoke. He kneeled down and held out his hand, "I'm Carson. I hear you're the special guest."

She hesitantly held her hand towards his, "I-I-I guess…" she whispered and finally shook the man's hand. He didn't seem scary. He actually seemed nice. And he didn't have a weapon so he couldn't be as bad as the mean man who had wanted to hurt her when she had first come there.

Carson picked the girl up and set her on a medical table nearby. "Now, how about telling me your name?"

"Zaira…"

"Isn't that a lovely one?"

Elizabeth smiled, "It's like Sara…it means princess."

"Ah, and ya look like a little princess," Carson told the girl smiling. "Ya just need a crown."

Zaira smiled. "Really?"

He nodded, "Now, I'm gonna to do a test, okay? I need to make sure you're not sick or anything. It'll hurt for a second, but that's it," he said as he got his things ready in order to draw blood.

Her smile fell, "NO! I don't like shots! PLEASE! I'm not sick! I'm not!" she cried completely terrified.

Elizabeth sat behind the girl and held her trying to comfort her, "Shhh…it's okay. I promise. Carson will be very gentle."

"NO! PLEASE! I'm NOT sick!"

Carson frowned, but took the advantage of Elizabeth keeping the girl somewhat still and was able to draw a vial of blood. "See, that wasn't so bad…"

Zaira just cried.

"Honey, how about telling me how you got here?" Elizabeth questioned rocking the girl a bit.

"I've always been here."

"You've always been where?"

"At-lan-tis…"

"Honey, you know where you are?"

Zaira nodded, "Home."

Elizabeth just stared at the girl, "This is home?"

"Yes."

"How did you get to Atlantis?" Carson tried again. She was obviously a confused little girl and didn't know what she was saying.

"Where did I go?" Zaira asked him looking worried.

"Did you use the Stargate? A jumper?"

Zaira frowned, "Is this a test? I'm not allowed to play with the Stargate controls or in the jumper bay…"

Carson put his hand on Elizabeth's shoulder and guided her a distance away. "Perhaps she's been traumatized in some way or is merely confused. Maybe you should try questioning her later…or even see if someone else more…child-like could get more out of her. We may even want to have her evaluated. I mean, she knows so much about Atlantis…"

"Yes, that worries me. Perhaps I should check with Teyla…maybe it's a child that was accidentally brought here or belongs with the Antholosians."

"Yes, that could be an idea, but," Carson started. "She's not dressed like an Antholosian."

Elizabeth just looked at him for a minute before looking back at the girl. He was right. And her clothing was crisp and clean. "Can you keep her here while I go find Teyla?"

Carson frowned, "I don't think she'd take very kindly to you leaving her here, she's already stated she doesn't like it here."

"Yes, she said that before she came in… Like she knew what you were going to do…" Elizabeth said slowly thinking about it. "There's something very odd and out of place about her."

"Well, she seems to like you, why don't you talk to her?" Carson suggested. "Take her with you, maybe walking would do you both some good."

Elizabeth nodded; she walked back over to Zaira and helped her down before taking her hand once again. "How about a walk?"

"As long as we get to go away from here," she said looking back at Carson as they left. She didn't like being poked.

Elizabeth had found Teyla and Major Sheppard in the gym and had left Zaira at the door while she talked to them, "Are you /sure/ she's not one of your people?" she asked.

"I am positive, Doctor. She's not even dressed like my people," Teyla pointed out.

"She looks more like an Atlantean," John said adding his two cents.

Elizabeth just stared at him, "You're not serious."

John shrugged, "Well she did say that this was home, didn't she? She knew that this was Atlantis and she was afraid of the medical bay before you entered with her. She…knows…things…"

Teyla just looked at him, "What are you suggesting?"

"Time travel," Elizabeth said. "But why just her? And why just appearing like that? In the past SG-1's time-traveled using the Stargate and solar flares… The Stargate wasn't activated."

"Hey, I like my idea. She's cute anyways," John said smiling over at the little girl and waving at her. He smiled more when she waved back. "Ya know…she actually looks a lot like you, Elizabeth."

Elizabeth frowned, "She's not mine. I think I would remember having a child and raising them."

"You sure?"

"John—"

"Okay, okay…it was just an idea…geez…"

Teyla smiled. "What will you do with her if you don't know where she belongs?"

"I don't know yet," Elizabeth admitted. "She's been a bit shaky about other people. Bates scared the hell out of her when she first showed up. I really don't know. I was hoping she was Antholosian. I don't know what we'll do now. We'll have to find some temporary home for her."

"Well, you seem to be doing a good job," John told her. "I elect you."

Elizabeth just stared at him, shocked at what he had just said.

"I agree, she does seem very comfortable with you," Teyla added.

Elizabeth sighed and watched as Major Sheppard walked over to the girl. She just stood there with Teyla thinking about how she was supposed to take care of this child and still do her duties on Atlantis. Though, she had an idea to make John help as he seemed to also do well with the girl.


	2. Chapter 2 Technical Difficulties

**Author:** atlantis child

**Title:** The Heirs to Atlantis

**Chapter Title:** Chapter 2 "Technical Difficulties"

**Summary:** Major Sheppard and Doctor Weir are quite confused at new arrivals that appear on Atlantis. They know too much for strangers.

**Genres:** Alternate Universe, Angst, Drama, Future Fic

**Rating:** PG

**Warnings:** none

**Author's Note: **This is my first Atlantis fic, and I am new with the show as my bio says, so I apologize for any mistakes I make regarding Atlantis or the people therein. Please, if you'd like to let me know, please do so kindly ;)

"Are you going to be okay?" he asked quietly when Elizabeth approached him. She had seemed so unsure about taking responsibility of the girl.

"She's asleep," she told him. Elizabeth had put Zaira to sleep in her bed. She was relieved that Zaira fell asleep rather quickly. She had worry written all across her face, she wasn't sure about caring for this child.

John frowned, "Are you going to be okay?" he repeated.

"I've only ever taken care of a dog. Somehow taking care of a child seems vastly different." She sighed and sat down, "What are we to do with her, John? If she didn't come through the Stargate is not Anthosian… It's like she appeared out of thin air."

"You'll do great, Elizabeth," he told her trying to be reassuring. "And I agree it is like she just appeared out of nowhere."

"But what do we do? I mean, do we continue to take care of her? Do we keep her here on Atlantis? Or do we start to look for people who would act as foster parents?"

"Maybe Carson will have more clues tomorrow. He has to be able to tell us /something/ from his tests, right?"

Elizabeth frowned, "I suppose. But he can't tell us what I want to know. Who the girl's parents are…where they are…and how did she get here?"

"And those are…good questions," Sheppard told her. "But for now I think it's best for her to stay with you… She /likes/ you, Elizabeth…and maybe she'll open up more to you." He moved over and sat next to her.

"Have I mentioned I have a dog on Earth, and I don't have kids?" Elizabeth asked looking up at him.

John smiled and wrapped his arm around her pulling her closer. "You're going to be a great mother some day," he told her and kissed her forehead.

"Oh yeah? And how do you know that?" she asked in a disbelieving tone.

"You've taken care of all of us, haven't you?" he pointed out still holding her.

Elizabeth had relaxed and let her head fall to his shoulder, "It's been a group effort."

John smiled, "That's called family, Elizabeth."

The lights in Atlantis started to flicker on and off at about four a.m., even the lights that had been off came on. "What the hell!" was Major Sheppard's response when he blinked his eyes open. It took him a minute to realize where he was. He was still in Elizabeth's quarters. Still holding her. "Elizabeth," he whispered nudging her a bit.

"Mmm?" she mumbled opening her eyes to be in pitch black one second and bright light the next.

"Did you remember to pay the electric bill?"

After a minute, Elizabeth had fully woken up and was sitting up trying to see if the lights would make up their mind.

"Maybe we shou—" John started, but was interrupted by a scream. Immediately, John hurried to where Elizabeth had laid Zaira down in her bed. He found her curled up under the blankets. "It's okay," he whispered as he scooped her up. "The lights are just broken."

Elizabeth had followed, but had stayed back as John looked like he was doing fine on his own.

"I don't like the dark," Zaira whispered.

John held her close using one hand to hold her against him, her arms were wrapped tightly around his neck and he doubted she was going anywhere. He reached out and took Elizabeth's hand pulling her along with him. "Let's find out what's going on."

"Please don't let the Wraith get me," the girl whispered into Sheppard's ear.

"Shh…the Wraith aren't here. One of the batteries is probably just having a fit," he tried to sound convincing. The girl's fears got him a bit and unconsciously, he held Zaira closer and held onto Elizabeth's hand tighter.

"The Wraith come in the dark," she whispered.

"Rodney, what's going on?" Elizabeth asked immediately when they entered the control room.

"I don't know! Nothing's making sense! And I think that the power to access the computer main frame from here has been re-routed," he told her quite frazzled and quite quickly.

"What do you mean?" Sheppard asked still with Zaira in his arms. He had let Elizabeth's hand go since the area was small and she couldn't go far.

"How is that possible?" Elizabeth added moving towards Rodney who was working with Zelenka.

Rodney was extremely frustrated. He was trying to figure out what the hell was happening, but constant questions weren't helping. "I don't know. Maybe Atlantis is going on strike," he said sarcastically.

"Rodney—" Sheppard started annoyed with McKay.

"What? The only other ideas I can come up with are that either someone's hacked into Atlantis or there's an intruder who knows the Atlantis systems."

John coughed a bit feeling the girl's hold around his neck tighten. He knew what she was thinking. "Don't worry, Honey… The Wraith aren't here…" he told her in a soothing tone. Teyla would have sensed their presence and reported it by then.

"Should she /really/ be here?" McKay asked.

"Rodney," Elizabeth spoke up. "/Focus/. We need to know what is going on right now."

"Look!" McKay started and then stopped when information came up on his screen.

Seeing the look on Rodney's face, Elizabeth started to worry. "What? What is it?"

"The shield…" Rodney stammered.

"Someone's turned on the shield," Zelenka stated.

"Do we at least know where the controls have been routed?" Elizabeth asked not liking that they didn't have control of Atlantis.

"Give me a minute," Rodney muttered trying to get things to cooperate. "Oh…CRAP!" he shouted just as the city jolted and started to sink into the ocean. He suddenly got a curious look on his face once they had stopped moving. "How did they figure out how to do that?" He hadn't even figured out how to re-anchor Atlantis to the bottom of the ocean.

John had fallen when Atlantis shook gracefully onto his butt, but had made sure that he held Zaira tightly and that no harm came to her.

"The Wraith can't come now," Zaira whispered.

"Yeah…" he said letting out a shaky breath and looking at the child a bit worried. Did she know about this?

"Well…we're on the bottom…again," Rodney announced a bit shakily.

"Doctor Weir?" Zelenka said aloud seeing her still on the ground. She had fallen during the city's decent, while those at consoles had just held onto them and braced for it. But she still wasn't moving.

"Elizabeth?" John called out as he got up separating from Zaira so that he could go to Elizabeth's side. He reached over and felt for a pulse. There was one…at least he thought it was one. "Elizabeth?" he said again hoping that she'd stir. He carefully to started to move her, but stopped when he saw the blood on his hands when he slipped his hand under her head. "We need to get Beckett down here!"

"Radios are down," someone reminded quietly.

"You'll have to take her to Beckett yourself," Zelenka told him.

"Go," Rodney said. "We'll work on at least getting radios up."

"I think Elizabeth would want complete control of Atlantis back," Sheppard said as he carefully picked Elizabeth up.

"We'll work on it," he told Sheppard.

"Stay close, Zaira," John said looking down at the little girl as he headed out of the control room. He didn't like this. He knew that a head wound was bad and bled heavily. He wished the power wasn't fluctuating and that he could use the transporter, but with the power like it was it was out of the question.

She did, "We're taking the long way to the scary place…" Zaira pointed out.

"Ya know, I don't think Carson would appreciate you calling his medical bay 'the scary place'," John told her looking down at her while they walked. "And the batteries still aren't working, so we have to take the long way."

"But it is the scary place!"

John smirked, "I know… But it's also a good place, we're gonna get Elizabeth fixed up."

Zaira looked up at him, "She'll be okay, right?"

"Of course she will," John tried to assure the girl. God, he prayed she'd be okay. As much as Elizabeth Weir could be a pain, he loved her…and he respected her. She was a good leader. Of course they would often agree to disagree, but he couldn't imagine Atlantis without her. She had to be okay.

She had to.


	3. Chapter 3 We Agree to Disagree

**Author:** atlantis child

**Title:** The Heirs to Atlantis

**Chapter Title:** Chapter 3 "We Agree to Disagree"

**Summary:** Major Sheppard and Doctor Weir are quite confused at new arrivals that appear on Atlantis. They know too much for strangers.

**Genres:** Alternate Universe, Angst, Drama, Future Fic

**Rating:** PG

**Warnings:** none

Major John Sheppard sat outside the medical bay after being told quite bluntly to get out by Carson. Apparently they were in the way. But dammit, he was worried about Elizabeth. He had been staring at the door ever since he had been ordered out with Zaira. It still bothered him that she knew things… How could she possibly know so much about Atlantis? Know about the Wraith?

Zaira just studied the man. She was sure if he was angry or not…he sorta seemed that way. But why would he be? Everything was going to be okay, Elizabeth was in the scary place, but the scary place was going to make her better…

"How do you know about Atlantis?" John asked not moving his gaze. He needed to know. What if this small child was somehow involved with everything that had started. It had started after they found her. Maybe there was a connection and he just wasn't seeing it yet.

"It's my home," she told him frowning. "Everyone knows about their home. Atlantis is mine."

He didn't like that answer. "No, Atlantis isn't your home… You'd have to be an Atlantean or something…"

Zaira just stared at him with her bright green eyes.

Her eyes were like piercing, he felt like she could see into his soul or something. He could feel them on him and turned to her. "You're not, are you?"

"We all are… Aren't we?" her voice was soft and calm, her eyes still bright as she talked to him.

"That's weird for a little girl to say…" he commented aloud staring at her.

"Is it?"

John nodded, "You sure you don't know anything about what's going on? Is there someone else here in the city?"

"I dunno… How would I know?" Zaira asked looking curiously at him.

"I think you know," he pressed.

The girl tilted her head looking at him, "But I don't."

"Are the Wraith here?" he asked even though he knew if they were Teyla would have probably tried to find someone and report it by now.

"The Wraith can't come to Atlantis when it's under water," she told him.

"I'm pretty sure they could."

Zaira moved so she had her feet underneath her so she could look at Sheppard without straining her neck. "How do you know?"

"Because I do."

"I think you're lying."

"You do, do you?"

Zaira nodded quickly, "Just because I'm a kid doesn't mean I'm stupid."

"Oh yeah?"

"Yeah."

Sheppard was about to go on and yell at her about being a brat and avoiding questions and saying that he knew that she knew about what was going on when she spoke first.

"The doctor's coming," Zaira told him getting up and heading for the door right as Carson walked out. She wrapped her arms around his leg hugging it tightly.

"Hi there, Lass. Don't be scared…Elizabeth is gonna be just fine. Don't fret," Carson said smiling down at the girl.

"He's mean," she whispered looking over at Sheppard.

"Is he now?" Carson asked looking from the girl to the major only to receive a nod from the girl.

John just got up ignoring them both and pushed past Carson entering the medical bay to find Elizabeth whether he liked it or not. He was sick of Zaira and her kiddy mind games; he just wanted to see that Elizabeth was okay.

Carson sighed and took Zaira's hand leading her into the medical bay, but keeping back. Sheppard was obviously not happy, and the Scottish doctor was smart enough to steer clear of the American.

Finding her rather quickly, John pulled a stool over and sat down at her bedside. She was still unconscious it seemed, but Carson had obviously repaired whatever Elizabeth had cut open. "Hey Elizabeth," he whispered gently picking up her hand and holding it between his. "We're underwater again, can you believe it?"

Picking Zaira up, Carson picked her up and set her on the edge of one of the beds. He tapped her nose, "I know something special about you," he told her with a bright smile. "You have the ancient gene. Did you know that?"

Zaira nodded, "Atlantis is my home."

"Do you know that Major Sheppard and I also have the gene? That makes the three of us special in a way…"

"I don't think he'll like me more if he knows…" Zaira said frowning. "He thinks it's my fault Atlantis is broken…"

Carson frowned, "It's not broken, Lass. And the major is just worried about Elizabeth. See, now that he's seen her he's fine. Rodney will have the city back online soon."

"He still doesn't like me anymore," she whispered dropping her head and just staring at the floor.

It was dark. Or at least it seemed dark. Elizabeth felt weak. She slowly attempted to open her eyelids. Slowly, but surely she managed. She saw John sitting there and could feel her hand in his. Squeezing his hand a bit, she smiled when she saw him open his eyes and a confused look settle on his face until he looked down at her. "Hey…" she managed to get out, her voice weak.

"Hey," he responded a smile spreading across his face, "Feel better?"

"I'm tired and have a massive headache, but other than that…"

"Well you hit your head pretty hard," he told her. "Atlantis is at the bottom of the ocean again."

"I know…I heard you," Elizabeth told him a small smile forming. "Thank you for staying with me…"

John smiled at her and rubbed her hand between his. "I haven't checked on the scientists, but I'm sure they're still working on it. Rodney'd probably just tell me to shut up and get out of his way anyways…"

"Where's Zaira? Don't tell me you left her in a room by herself," Elizabeth said getting a bit worried.

He sighed, "No. She's asleep over on the other side of the room. Carson's been keeping an eye on her." He stopped for a minute before continuing on, "I think Zaira knows what's going on here…"

"John, she's like six," Elizabeth said very disbelieving.

Carson walked over interrupting. "Good to see you awake." He looked from Elizabeth to John and then back to Elizabeth. "Did the major inform you that he's scared the little girl?"

"John—"

"Hey! It's not my fault that she knows so much. Someone has to ask the questions. She knows about Atlantis and the Wraith," John went on, "She said that we'd be safe underwater from the Wraith when the city sunk."

"She has the gene," Carson informed them. "Perhaps that is why she knows so much."

"But having the gene doesn't give her that information," Elizabeth argued. She didn't want to think of the little girl as an enemy. How could she be? She was far too small and innocent.

Carson sighed, "No, it doesn't. But she also hasn't opened up to anyone it seems. And you may have very well blown that, major." He shook his head before leaving. He'd check on Elizabeth later.

John grumbled before looking back at Elizabeth, "I swear I was just asking questions."

"But she's a child, John. You can't just question her like you would anyone else," Elizabeth argued.

"I was being good about it!" he defended. "She was arguing right back at me!"

Elizabeth sighed, "We have to find out who is doing this and how and stop them. We need control of Atlantis back."

"Agreed."

"I don't think it's her, John. I don't think she knows anything. I think she would have said more if she did."

"And that's where we disagree…"

Elizabeth sighed. This was not going to be easy, especially if Carson kept her.


End file.
